Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rhodopseudomonas palustris CGA009

ABSTRACT: Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing

PROVIDER: PRJNA169623 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR517910.fastq.gz	Fastqsanger.gz
	SRR517911.fastq.gz	Fastqsanger.gz
	SRR517912.fastq.gz	Fastqsanger.gz

Items per page:

1 - 3 of 3

Similar Datasets

Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris

Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Keywords: Comparison of transcriptome profiles

2008-05-07 | GSE6221 | GEO

Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris

2008-05-07 | E-GEOD-6221 | biostudies-arrayexpress

Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing

Project description:High-throughput sequencing of cDNA prepared from RNA, an approach known as RNA-seq, is coming into increasing use as a method for transcriptome analysis. Despite its many advantages, widespread adoption of the technique has been hampered by a lack of easy-to-use, integrated, open source tools for analyzing the nucleotide sequence data that are generated. Here we describe Xpression, an integrated tool for processing prokaryotic RNA-seq data. The tool is easy to use and is fully automated. It performs all essential processing tasks including nucleotide sequence extraction, alignment, quantification, normalization and visualization. Importantly, Xpression supports multiplexed and strand-specific nucleotide sequence data. It extracts and trims specific sequences from files and separately quantifies sense and antisense reads in the final results. Outputs from the tool can also be conveniently used in downstream analysis. In this paper, we show the utility of Xpression to process strand-specific RNA-seq data to identify genes regulated by CouR, a transcription factor that controls p-coumarate degradation by the bacterium Rhodopseudomonas palustris.

2012-09-01 | GSE39025 | GEO

Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris using Xpression, an integrated tool for prokaryotic RNA-seq data processing

2012-09-01 | E-GEOD-39025 | biostudies-arrayexpress

Rhodopseudomonas palustris CGA009

Project description:Rhodopseudomonas palustris Tn-seq Library

| PRJNA301497 | ENA

Rhodopseudomonas palustris CGA009

Project description:Rhodopseudomonas palustris CGA009 Raw sequence reads

| PRJNA359692 | ENA

Rhodopseudomonas palustris

Project description:Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris

| PRJNA97539 | ENA